The GENSTRUCTURE/bionet.genome.gene-structure newsgroup is ready for
operation. This newsgroup is moderated, i.e., all postings are
forwarded to a moderator/editor and are reviewed prior to
distribution. The newsgroup charter is appended below followed by
detailed usage instructions and information on how to search the
newsgroup archives. *Please save* this message for future reference
if you intend to participate in this newsgroup.
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Proposal for GENSTRUCTURE/bionet.genome.gene-structure (moderated)
Proposed USENET name: bionet.genome.gene-structure
One line Description: Genome and chromatin structure and function
Status: Moderated
Proposed Moderation address: bionet-genome-gene-structure at net.bio.net
(genstruc-moderator at net.bio.net
is an alias for
bionet-genome-gene-structure at net.bio.net)
Moderator: Graham Dellaire
Proposed mailing list name: GENSTRUCTURE
Proposed e-mail addresses: genstruc at net.bio.netgenstruc at daresbury.ac.uk
Charter:
The purpose of the GENSTRUCTURE newsgroup is to provide a proper forum
for the discussion of issues pertaining and involving genome and/or
chromatin structure and function (see _Topics of Discussion_).
Primarily it should enable those researchers who work in
genome/chromatin structure or related fields to communicate ideas and
information, as well as, provide a chance for collaboration among
national and international research groups.
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Topics of Discussion include:
1. Genome/chromatin accessibility and recombination
-recombination hotspots (mieotic and mitotic)
-fragile sites
-imprinting and recombination rates
-ectopic gene targeting and chromatin structure
2. 3D-organization of the nucleus
-chromosome territories
-nucleoli
-nuclear lamina (telomere localization)
-tissue or cell cycle dependent
positioning of chromosomes
-RNA tracking
3. Effect of Superhelicity and DNA topology/structure(Triple strand, Z-DNA,
cruciform, bent etc) on biological processes such as:
-replication
(ex. replication fork barriers, initiation sites)
-transcription
(ex. promoter function in relation to superhelicity)
-recombination
(ex. Gin and Hin invertases and superhelicity)
4. Histones and Nucleosomes and chromatin structure/function
-H1 repression of transcription
-Post translational modification of histones
acetylation (H4, H3), phosphorylation (H1, H3)
and ubiquitination (H2A, H2B)
-Histone variants (ex. H2A.Z in mammals, H5 of chicken)
5. Models of genome structure (Loop Domain Model, Channel Model,
MegaBase Giant Loop Model, etc.)
6. Classical chromosome elements and their relationship to gene function
-centromeres (constitutive heterochromatin and
gene silencing)
-telomeres (associated silencing and involvement
in position effect)
7. Evolution of the Genome
-isochores and base-content (GC vs. AT)
-formation of gene clusters and syntenic mapping
-repetitive elements (satellites, telomeric and
centromeric (alpha) repeats, lines and sines)
8. Biologically important mutants and knockouts that affect
genome/chromatin structure
-ex. SNF/SWI, TOPO mutants in yeast
-RAD 51,52,54 knockout mice
-AT, BLM, FA mouse models
9. Techniques for genome/chromatin analysis
-cytogenetic techniques (g banding, r and q)
-Fluorescent In situ analysis(FISH)
-Confocal microscopy
-Electron microscopy
-Electron microscopy In situ analysis (EMISH)
-psoralen, polyamine crosslinking
-In vivo nucleosome foot printing
-Dnase I/Micrococcal Nuclease sensitivity
-VM26 Topoisomerase II site mapping
10. Chromatin/DNA binding proteins and their effects on chromatin structure
and/or gene expression
-Polycomb proteins
-Rap1 (telomere silencing)
-alpha2-MCM1 (repression of MAT locus)
-CENP A/B/C (centromere structure/function)
-XCAP-C/E, SMC1/2 (chromatin Condensation)
-remodeling of chromatin by SWI/SNF proteins
-H-NS in bacteria (role in nucleoid topology
vs. gene function)
11. Nuclear Matrix (NM) and Nuclear Lamina (NL)
-cell cycle regulation of formation of NM and NL
-transcription and replications factors
and the concept of a dynamic NM
(ex. tissue and temporal specificity)
-role of NM in signal transduction
(mechanistic vs. chemical signals)
12. Matrix attatchent regions (MAR's), domain boundaries and locus
control regions (LCR's) and their relationship to gene structure
and function.
-definition of transcription/replication domains
-model systems ex. betaglobin (LCR) SCS/SCS' of
the Drosophila Heat Shock Locus (HS87a7)
13. Phenomenon of Position Effect and Transvection
-in drosophila (HP1, polycomb, heterochromatization)
-in mammalian systems (silencing or variegated
expression of transgenes)
-in fungi
14. Epigenetic effects on gene function
-imprinting
-methylation
-maintenance of early/late replication
15. Dosage compensation mechanisms and X chromosome inactivation
-MSL proteins of Drosophila
-XIC (Xist RNA) in mammals
-CpG methylation
16. Chromatin structure and DNA replication
-ORC1 protein of yeast
-origins of replication
(association with cruciform, bent DNA and MARS)
17. Specialized methods of nuclear packaging
-bacterial nucleoid
-packaging of DNA in spermatozoa
18. DNA repair and chromatin structure
-TFIIH (transcription coupled repair)
-p53
-BLM and AT genes
-poly-ADP-polymerase (PARP)
19. Mechanisms of genomic instability
-during oncogenesis
-process of chromosomal aberration (stable and unstable)
(ex. role of micronuclei in the process)
-chromosomal aberration during aging and mechanisms
of instability (ex. telomeres and telomerase)
In addition this newsgroup provides:
A forum for the exchange of information about future congresses
and meetings in areas of molecular biology relating to genome
structure/function.
A forum for the exchange of information about textbooks, internet
resources, visual materials, and computer programs.
A source of quick help for last-minute troubleshooting,
sources of materials, and practical advice; in areas such as
-Specific common resources
(ex. primers, antibodies, vectors)
-Genome analysis techniques
-Transgenic models and mutant cell lines
Moderation Policy:
Mass-posted commercial messages, chain letters, and similar postings
not associated with or pertaining to the study of genome/chromatin
structure and function will be deleted without comment. Inappropriate
messages posted in good faith will be returned to the sender.
Messages not strictly within the charter but likely to be of interest
to many subscribers (e.g., messages dealing with transcription and
replication factors) will be accepted.
Subscribers are welcome from universities or any academic
institutions, government agencies, medical institutions, and
industrial or commercial organizations. Contributions within the
functions outlined above are encouraged.
Proposed discussion leaders:
*Note: Area of expertise is written in brackets
Graham Dellaire, e-mail: dellaire at odyssee.net (gdella at po-box.mcgill.ca)
Institut du Cancer de Montreal
Centre de Recherche L.C. Simard
1560 Sherbrooke Street East,
Montreal, Quebec, Canada H2L 4M1
telephone:1 (514) 876 6936; fax: (514) 876 5476
*(Expertise:chromatin structure and recombination; Recombination
Access Mapping (RAM); genome structure analysis)
Ronald Hancock, e-mail: ronald.hancock at crhdq.ulaval.ca
Professor
Laval University Cancer Research Centre
1 rue de l'Arsenal
Quebec, Canada G1R 2J6
telephone: 1 (418) 691-5281; fax: 1 (418) 691-5439
*(Expertise:genome organisation in vivo; models of genome structure;
topoisomerases; VM26 topoisomerase II site mapping)
Eric Milot, e-mail: milot at ch1.fgg.eur.nl
Faculty of Medicine
Dept. of Cell Biology and Genetics
P.O. Box 1738
3000 DR Rotterdam
The Netherlands
telephone: 3110 4087164; fax: 3110 4360225
*(Expertise:Chromatin context and transcription; Polycomb
protein; position effect variegation; chromosome and nuclear
organisation; dosage compensation)
**Tentative Discussion leader**
Peter Cook, e-mail: peter.cook at pathology.oxford.ac.uk
Professor of Cell Biology,
The Sir William Dunn School of Pathology,
South Parks Road,
Oxford, OX1 3RE, UK.
Telephone (direct line) : +44/0 1865 275528
Telephone (switchboard) : +44/0 1865 275500
Fax : +44/0 1865 275501
http://www.molbiol.ox.ac.uk/www/users/counsell/cook.htm
(Expertise:Chromatin/Genome Structure and Function in regard to
transcription and replication)
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